BN1351 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 8.5146e-06 2.0670e-03
Layer 2 1.6690e-05 1.7700e-03
Layer 4 1.9504e-04 6.5016e-04
Layer 5 2.7074e-04 1.3840e-03
Layer 6 1.1444e-03 2.7309e-02
Layer 1 1.2520e-01 1.4812e-01
WM 9.9996e-01 5.6402e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
CHN1 Expression Distribution
Gene Specificity Score (GSS)
CHN1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
CHN1 Layer 4 3.0312 0.7808
UCHL1 Layer 4 3.2852 0.7786
CALM3 Layer 4 3.0312 0.7765
EEF1A2 Layer 4 3.2637 0.7731
CALM2 Layer 4 2.8223 0.7725
PKM Layer 4 3.2500 0.7716
SYN1 Layer 4 3.3145 0.7711
VSNL1 Layer 4 3.1191 0.7696
HSP90AB1 Layer 4 2.8027 0.7694
SNAP25 Layer 4 2.8086 0.7665
CFL1 Layer 4 3.0996 0.7652
SNRPN Layer 4 3.1328 0.7646
TPI1 Layer 2 2.6719 0.7636
TSPYL1 Layer 4 3.3066 0.7633
UBB Layer 2 2.7188 0.7631
FAIM2 Layer 4 2.9473 0.7614
PPP2R1A Layer 4 2.8086 0.7609
NORAD Layer 4 2.8770 0.7608
ARPP19 Layer 4 2.8027 0.7608
RTN3 Layer 4 2.7969 0.7606
EIF1 Layer 4 2.7363 0.7597
SLC17A7 Layer 4 2.8281 0.7595
ACTG1 Layer 3 2.8652 0.7591
OLFM1 Layer 2 2.9922 0.7582
PLD3 Layer 4 2.7188 0.7579
ARL6IP1 Layer 4 2.9531 0.7575
SERINC1 Layer 4 3.0059 0.7574
STMN1 Layer 4 3.7148 0.7572
GDI1 Layer 4 3.0449 0.7569
RUNDC3A Layer 4 2.8770 0.7568
UBC Layer 4 2.8770 0.7555
APLP1 Layer 4 2.7793 0.7549
BSG Layer 2 2.6777 0.7543
PHYHIP Layer 2 2.7012 0.7537
PRKAR1B Layer 4 3.0996 0.7527
CAMK2B Layer 4 2.7852 0.7522
RTN4 Layer 2 3.0059 0.7521
PRNP Layer 4 2.9863 0.7518
PPIA Layer 2 2.6484 0.7515
TMSB10 Layer 4 2.9023 0.7510
MAP1A Layer 3 2.7910 0.7507
JUND Layer 4 2.6309 0.7500
SLC22A17 Layer 4 2.6777 0.7496
ATP6V0C Layer 4 3.0996 0.7493
NDFIP1 Layer 4 2.7480 0.7488
MAP1B Layer 5 2.7852 0.7482
PSAP Layer 4 2.8594 0.7482
GPX4 Layer 4 2.5273 0.7479
TSPAN7 Layer 4 3.0117 0.7479
NPTXR Layer 2 2.6484 0.7472

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1351
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1351_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1351/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1351/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1351/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1351/report/PD/BN1351_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1351/report/PD/BN1351_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:46:30
  • Number of Processes: 10
  • Spending Time: 0h 4m